Looking at the various arguements brought forward, I am going ahead with the "let bitcoind manage" the transactions approach using the "Accounts" feature as a means of storing balances. At the moment I'd rather deal with scalability issues vs having unscynchronized balances between a separate DB vs wallet.dat.
If you want to scale really big with this approach you need several servers each running bitcoind, and each managing their share of accounts. A load balancer for this setup is fairly trivial to set up.
Load balancing is definitely one method and it has crossed my mind, but that would defeat the "move accounts" feature that provides instantaneous transfer for users within the system (same wallet.dat). Having multiple bitcoind instnaces and moving counts from one wallet to other would also create additional network transactions in addition to delays required for confirmations.
